2NY1

HIV-1 gp120 Envelope Glycoprotein (I109C, T257S, S334A, S375W, Q428C) Complexed with CD4 and Antibody 17b

Structural Biology Knowledgebase: 2NY1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.209

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2NY1

Classification: VIRAL PROTEIN / IMMUNE SYSTEM

Total Structure Weight: 106807.34

Macromolecule Entities
Molecule Chains Length Organism Details
ENVELOPE GLYCOPROTEIN GP120 A 317 Human immunodeficiency virus 1 Fragment: CORE
Gene Name(s): env
T-cell surface glycoprotein CD4 B 184 Homo sapiens Fragment: D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Gene Name(s): CD4 Gene View
ANTIBODY 17B, LIGHT CHAIN C 214 Homo sapiens Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Gene Name(s): IGK@
ANTIBODY 17B, HEAVY CHAIN D 229 Homo sapiens Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Gene Name(s): DKFZp686I15212

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SUC
Query on SUC

D SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.209
  • Space Group: P 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 71.11 α = 90.00
b = 88.16 β = 90.00
c = 197.67 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-11-20
  • Released Date: 2007-02-06
  • Deposition author(s): Zhou, T., Xu, L., Dey, B., Hessell, A.J., Van Ryk, D., Xiang, S.H., Yang, X, Zhang, M.Y., Zwick, M.B., Arthos, J., Burton, D.R., Dimitrov, D.S., Sodroski, J., Wyatt, R., Nabel, G.J., Kwong, P.D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update